* Macro cleanup and obvious warning fixes in parallel code.
* Moved H5FD comm and info dup/free wrapper code to a new H5mpi.c file
and separated it to deal with each MPI type separately.
* Changed return type of H5FD_driver_query() to herr_t.
* Updated swmr.c to use H5FDdriver_query() instead of the private call.
* Added some flags tests to vfd.c.
* Moved H5FD_driver_query() to H5FDint.c.
* Minor typo fixes in H5I.c.
* Updated swmr.c to check the VFD feature flags and skip the
retries test when the VFD is not compatible with H5P_DEFAULT.
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
(https://jira.hdfgroup.org/browse/HDFFV-10055).
Briefly, in H5C_collective_write() in H5Cmpio.c,
the metadata cache attempts to perform a collective
write of metadata cache entries.
This worked fine as long as all processes had at
least one entry to write.
However, when the process has no entries, the
function tries to participate in the collective write
by calling MPI_File_set_view(),
MPI_File_write_all() and then MPI_File_set_view()
again, to match the calls in H5FD_mpio_write().
After pull request 183, the CGNS test benchmark_hdf5
started failing. On investigation, I determined that
the failure occurred in the first call to MPI_File_set_view()
in the "no data to write" path through H5C_collective_write().
Note that pull request 183 did not create the problem,
it only exposed it. The bug can be observed after pull
request 182 if one executes the CGNS progam
src/ptests/benchmark_hdf5 with 90 processes.
The problem appears to have been that the calls to
MPI_File_set_view() in H5C_collective_write() and
H5FD_mpio_write() were using different values for the
info parameter. I patched the problem by adding a
MPI specific VFD call allowing me to get the MPI_Info
used in H5FD_mpio_write() for use in
MPI_File_set_view() calls in H5C_collective_write().
Tested serial & parallel, debug & production on
Jelly.
Clean up warnings (from 2774 -> 1560, with my standard debug build)
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
- remove H5AC_ind_dxpl_id and use only H5AC_dxpl_id everywhere instead.
- remove flush_me_collectively flag from cache entries
- add a collective sanity check (MPI_Barrier) for every HDF5 API routine that could possibly touch the file. This is trigerred when the environment variable H5_COLL_API_SANITY_CHECK is set to a non 0 digit.
tested on BB-8 with serial and parallel.
Refactor property list code to "deep copy" properties in the correct way,
retraining the rest of the library to copy & release things correctly. This
cleans up another batch of memory leaks, etc. within the library.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
Linux/32 2.6.x (jam) w/serial & parallel
(h5committest forthcoming)
Clean up EOF code within library and add 'mem_type' parameter to 'get_eof'
VFD callback, to avoid various ambiguous situations, particularly with the
multi VFD. (Supports changes for 'avoid_truncate' feature also)
Tested on:
MacOSX/64 10.10.1 (amazon) w/serial & parallel
h5committest forthcoming
Make progress toward moving from DXPL IDs to property list structures
within the library. Also move the signature location code from the H5F
package to the H5FD package, where it's a better fit. Also, clean up some
more compiler warnings along the way.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel
(h5committest forthcoming)
Begin process of migrating from using property list IDs internally to the
library to using the internal generic property list data structure.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel
(h5committest forthcoming)
Remove all traces of MPI-POSIX VFD and GPFS detection/code.
Remove remaining traces of stream VFD.
Remove testpar/t_posix_compliant test (it's not actually verifying anything).
Clean up H5D__mpio_opt_possible() further.
Moved environment variable that disables MPI collective operations into
MPI-IO VFD (instead of it being in src/H5S.c).
A few other small code cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
Clean up file driver property handling, along with some misc. warnings.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/debug, gcc 4.7.1, C++, FORTRAN & threadsafe
(h5committest upcoming)
Bring sec2 and log VFDs back into agreement. Correct several compiler
warnings. Also add some additional statistics to the log VFD and promote the
parameter for H5Pset_fapl_log from 'unsigned' to 'unsigned long long'.
Tested on:
Mac OS X/32 10.6.6 (amazon) w/debug & production
FreeBSD/32 8.2 (loyalty) w/debug
FreeBSD/64 8.2 (freedom) w/debug
Fix a few more problems when the user block is not aligned properly.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Switch from using a 'flags' parameter to the flush routine(s), to just
using a single 'closing' boolean parameter, since that's all we're doing with
the flags anyway and this makes things more obvious.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Final merge of changes from sblock_mdc branch back to trunk. The superblock is now managed by the metadata cache.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Bring file free space branch changes through r15795 into trunk, which
includes a fair bit of code cleanup & rearrangement along with a couple of
bug fixes also.
Tested on:
Mac OS X/32 10.5.5 (amazon) in debug mode
Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
> 1.
Description: Added a new field 'app_count' to H5I_id_info_t struct, to track
the reference count on an id due to the application. the old 'count' field
tracks the total. Generally any id visible to the application gets placed
in app_count. Added app_ref boolean parameter to H5I_inc_ref, H5I_dec_ref,
H5I_register, H5I_clear_type, and a few other functions, to specify whether
the operation(s) being performed on the id(s) are due to the application
(TRUE) or not (FALSE). Test added for this case.
Tested: kagiso, smirom, linew (h5committest)
- Add hash value for skip list string types, to reduce # of string
comparisons.
- Fixed bug with metadata/small data block aggregator adding size == 0
block into file free space list.
- Refactored metadata/small data block aggregator code into single set of
common routines.
- Changed block aggregator code to be smarter about releasing space in the
'other' block when the 'other' block has aggregated enough data.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Clean up some of the file space allocation formatting.
Beef up the attribute creation order tests to make certain they are
handling shared atributes correctly (which they apparently are :-)
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
Code cleanup
Description:
Clean up various warnings reported by the Windows team.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
New feature
Description:
Search free list when checking for, or actually performing, extension of
an object in the file.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Solaris 2.9 (shanti)
Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
Code optimization
Description:
Allow global heap collections to grow in size (up to a 64K limit) if they
are able to. This allows them to grow to a more reasonable size than the 4K
minimum size.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
Code cleanup/optimization
Description:
Query property list values once, at the beginning of the I/O routines,
instead of querying the property list values multiple (lots!) of times in
lower level routines.
Solution:
Create "property list caches" for internal library queries of the property
list values.
Platforms tested:
IBM p690 (copper) w/parallel & fphdf5
h5committest
Bug fix/optimization
Description:
Address slowdown in MPI-I/O file metadata operations that was introduced
mid-stream. We now _require_ a POSIX compliant parallel file system for the
MPI-I/O file driver (as well as for the MPI-POSIX file driver).
Also optimized file open operation when the file is being created by
reducing the number of collective & syncronizing calls.
Additionally, refactor the MPI routines into a common place, eliminating
duplicated code.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
h5committest
Warning cleanup
Description:
Make a parameter 'const' to clean up a warning during compiles.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
Code cleanup
Description:
Refactored handlier of VFL drivers in file access and data transfer property
lists in order to simplify and unify the code dealing with them.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
